This thesis is principally an investigation on behavioural aspects of bracken control herbicides in some plant and soil systems with a view to improving their effectiveness. The main chemicals investigated were asulam and aminotriazole. As the work developed broader aspects were studied, including the behaviour of iodide and thiocyanate in plants. The work can be sub-divided as follows:- 1. A brief discussion of bracken and its control was made with some emphasis being placed on its control by systemic herbicides and possible approaches to improving their efficiency. 2. An investigation into the mechanism of action of asulam in plants. The findings can be summarized as follows:- Preliminary work involving lAA-oxidase assays and plant growth studies revealed an interesting interaction between e-aminobenzoic acid and asulam which indicated sulphonamide-type activity for asulam. A series of experiments were carried out whereby a range of species sown in beakers containing vermiculite were treated with asulam solutions. This resulted principally in stunting of the root system which could be partially or totally overcome by the simultaneous addition of either e-aminobenzoic acid or folic acid. Compounds related to e-aminobenzoic acid had no such activity, indicating the specificity of the antagonism. The results led to the conclusion that a possible mechanism of action of asulam is the inhibition of folic acid synthesis resulting in impairment of biological methylations and hence inhibition of protein and nucleic acid synthesis. The selectivity of asulam may be due to differential e-aminobenzoate or folate concentrations. 3. An investigation into the possibility of achieving pre-emergence activity for asulam in bracken control. as follows:- An appraisal of asulam soil behaviour was made, whereupon it The results can be summarized was considered that the use of additives would probably be required to regulate movement and prolong persistence for sufficient quantities to achieve contact with the rhizome buds. Asulam adsorption experiments, carried out using surfactant solutions and three acid-organic soils found under bracken, revealed that, on the whole, the anionic surfactants employed (sodium dodecyl sulphate and sodium dodecylbenzene sulphonate) significantly reduced asulam adsorption, whilst cetyl trimethylammonium bromide (cationic surfactant) significantly increased adsorption. These trends were reflected in leaching experiments using a thick layer soil plate method. Most surfactant treatments decreased persistence of asulam in nonleaching degradation experiments, sodium dodecylbenzene sulphonate being an exception. persistence. In a field trial, pre-emergence application of asulam No carbamate-derived additive had any effects on asulam (G.7 kg/ha) had no effect on bracken. The use of 1% cetyl trimethylammonium bromide or 1% sodium dodecylbenzene sulphonate in the spray formulations had no beneficial effect. 4. An investigation into the use of ammonium thiocyanate and other additives in bracken control formulations to reduce herb Established work had shown that scorching of bracken fronds by aminotriazole was a result of detoxification via a free radical mechanism and led to subsequent poor performance due to decreased translocation. A bioassay, involving floating bracken leaflets on aminotriazole solutions, was developed for assessing the effects of the free radical scavenger ammonium thiocyanate on aminotriazole scorching and assessing the activities of other potential additives. The results indicated that the concentration of ammonium thiocyanate, rather than the 1:1 ratio with aminotriazole at present used commercially, is the critical factor in determining the reduction in scorching. Further results revealed that the concentration of ammonium thiocyanate required could vary depending on the environment under which ~he bracken was growing. In a field experiment using 8.4 kg/ha aminotriazole and ammonium thiocyanate at a range of ratios from 1:0 to 1:1.25, only the 1:0.5 aminotriazole to ammonium thiocyanate gave significantly greater control than the aminotriazole alone after 3 years (74% control). Of other potential additives tested in the bioassay, thioacetamide was selected as promising for aminotriazole formulations, however, in a field trial it proved ineffective at the level used. Successful incorporation of asulam into the scorching bioassay proved difficult. In a field trial, an ammonium thiocyanate-asulam mixture (10:1) had no beneficial effect over asulam alone (2.2 kg/ha) at 2 spraying dates. Preliminary experiments involving the use of dock and potato leaflets, as material for the scorch bioassay, produced promising results for the tailoring of aminotriazole-ammonium thiocyanate formulations for improved effective control. 5. An investigation into the selective herbicidal activity of iodide. The results can be summarized as follows:- In initial studies, the rate of iodide oxidation in an in-vitro hydrogen peroxide/horseradish peroxidase system was found to be reduced by the addition of ammonium thiocyanate. The selective herbicidal activity of sodium iodide towards dwarf bean, pea, kale and cabbage was tested while the potential thiocyanate content of these plants was measured. A good relationship between increasing thiocyanate content and increasing resistance to iodide was observed. Further studies achieved limited success in conferring resistance to iodide in bean with thiocyanate additions, while the mechanism of inhibition of thiocyanate in the enzyme system was found to be ma~nly through chemical reduction of the iodine product - the toxic moiety. Evidence was gathered to suggest that other compounds present in plants, including glucosinolates, thiols and ascorbate, and some pesticidal additions, may contribute to the overall selectivity through their effect on iodine formation and/or persistence. 6. An investigation into the mode of action of iodide and thiocyanate in plants. The results can be summarized as follows:- Whole plant studies using dwarf bean reaffirmed that of the halides and pseudohalide thiocyanate, only iodide and thiocyanate possess defoliant properties. Established work had indicated their possible involvement with IAA (indole-3-acetic acid). In-vitro enzyme studies and photochemical and chemical oxidations of IAA, suggested that IAA destruction is not through a direct interaction between IAA and the halide and pseudohalide but depends on their conversion to the halogen or pseudohalogen which can then destroy lAA. This may be accomplished by the peroxidase enzyme system for iodide only and does not provide a mechanism for thiocyanate activity. However, both iodide and thiocyanate have chemical oxidation potentials suitable for their conversion to the halogen or pseudohalogen respectively via the photosynthetic apparatus. Hence, this provided an explanation for their activity and the apparent inactivity of bromide, chloride and fluoride which would be oxidised very slowly or not at all. 7. Some conclusions as to the outcome of the studies were drawn and some suggestions made for further work.

Two distinct biosynthetic pathways to the essential amino acid L-lysine (A) are found in nature. The -aminoadipate pathway operates in fungi and yeasts. The diaminopimelate (DAP) pathway occurs in bacteria and higher plants. Our studies were concerned with the DAP pathway and particularly with the first two steps of this pathway. These steps involve condensation of L-aspartate--semialdehyde (ASA) (B) with pyruvate (C) to form L-2,3-dihydrodipicolinic acid (DHDPS) (D) and subsequent reduction to L-2,3,4,5-tetrahydrodipicolinic acid (THDPA) (E). The first step is catalysed by the enzyme dihydrodipicolinate synthase (DHDPS). The second step is catalysed by the enzyme dihydrodipicolinate reductase (DHDPR) and utilises NADPH as a co-factor. (Fig 6269A) Our primary objective was the inhibition of this biosynthetic pathway. Inhibitors of this pathway have potential as antibacterial or herbicidal agents. A number of substrate analogues of the DHDPS and DHDPR enzymes were prepared and tested as inhibitors of these enzymes. In previous studies by our group, heterocyclic compound (F) showed promising activity. In our work, a number of analogues of compound (F) were prepared. Inhibition studies with these compounds constituted a valuable insight into the characteristics of these enzymes. The level of inhibition with these compounds and for a range of other substrate analogues indicate high substrate selectivity for the enzymes. (Fig 6269B) The condensation catalysed by DHDPS is mechanistically interesting. In chemical terms, C-C bond formation is commonly a high energy process involving highly reactive compounds such as organometallic agents or strong bases. In such cases the strategy must be directed towards protecting other functionality or introducing it at a later stage. Clearly, achieving this task under mild conditions with the high regio- and stereoselectivity associated with enzymic catalysis could be of tremendous advantage. Once again, however, we were restricted by the high substrate specificity of the DHDPS enzyme. In earlier studies by our group, Dr J.E. McKendrick found evidence of substrate activity for 2- and 3-methyl substituted ASA, (G) and (H), respectively. In our work, an improved preparation of these compounds was developed and the subsequent biotransformations with DHDPS were examined both qualitatively and quantitatively. Interestingly, compound (G) was shown to display a greater substrate activity than ASA. The preparation of ASA methyl ester (I) was achieved. This compound also displayed a moderate level of substrate activity and was the only compound found to show substrate activity for a DHDPS/DHDPR coupled substrate assay. (Fig 6269C) A significant proportion of our effort was concentrated on the investigation of glutamate--semialdehyde (GSA) (J), the higher homologue of ASA, as a substrate of DHDPS. Problems were encountered with earlier studies in this area because of cyclisation of GSA, even in protected forms. To counter this problem two novel strategies were considered. The first involved in situ enzymic deprotection of the N-acetyl derivative of GSA. Although this was successful for N-Acetyl-ASA, problems with cyclisation were once again experienced for the GSA equivalent. The second strategy utilises the reversible nature of enzymic catalysis. The synthesis of the proposed 7-membered heterocyclic product (K) of DHDPS catalysed condensation of GSA and pyruvate is not a trivial task. Some progress was made and further direction detailed. Further validation for this study was demonstrated on preparation of 5-hydroxyproline (L). Compound (L) is a cyclic equivalent of GSA and was found to display clear evidence of substrate activity. (Fig 6269D)

No description available.

Measurement of the Raman optical activity (ROA) spectra of biomolecules has become an experimental possibility due to significant advances in the available technology, and its successful implementation into the ROA instruments at the University of Glasgow. The ease with which the ROA spectra of biological molecules can be successfully measured lends itself perfectly to the ever-growing demand for biomolecular structural information, especially in the context of proteomics and the Human Genome Project. ROA spectroscopy is able to probe the chiral peptide backbone of proteins, and as such the ROA spectrum of a protein contains a wealth of structural information from within the whole molecule, across the whole vibrational spectrum. As well as containing detailed information from specific structural elements such as sections of secondary structure and motifs, the ability of ROA to see the molecule as a whole also enables the global fold of the protein to be deduced from the ROA spectrum. The development of the analysis of ROA spectra has largely been based upon the correlation of ROA spectra of proteins of known structure with structural information from alternative sources, chiefly X-ray crystallography and multidimensional nuclear magnetic resonance (NMR). As the database of ROA spectra of polypeptides and proteins has grown, it has been possible to tighten up the assignment of ROA spectral bands and band patterns to aspects of known structural content. With a basis for the correlation between the ROA spectrum and the known crystal structure (or NMR structure) being well established, it is possible to interpret the ROA spectra of proteins that do not have (for whatever reason) well defined structures. This means that ROA spectroscopy can provide invaluable structural information for proteins that are precluded from analysis by other techniques, and also cast new light on the structures of proteins that have not been well defined. In order to fully interpret an ROA spectrum of a protein, it is necessary to be familiar with protein structure and the ROA experiment as a whole. Analysing an ROA spectrum is a detailed and highly subjective process. Depending on the experience of the analyst, the information contained within the spectra can be extracted readily or not so readily. For this reason, it would be desirable to develop a technique that is capable of interpreting not only individual spectra, but also whole data sets in a manner that is independent of the analyst, and therefore independent of any preconceptions (or inexperience) the analyst may have. This project presents an up-to-date collection of newly obtained ROA spectra of a large number of proteins across a range of structural class types. In addition, the statistical technique of principal component analysis (PflA) has been used as a tool for the analysis of this new data. It is hoped that the result of this work will provide a basis for the future analysis of protein ROA spectra that is both mathematically rigorous and convenient.

No description available.

No description available.

The reactions of dichlorine and dibromine on compound semiconductors follow a pattern of halogenation of the substrate surface, followed by solvation of the halogenated products and removal of the secondary products in the etchant solutions. The reactions of hypochlorite and hydrogen peroxide follow a similar pattern, beginning with oxidation of the substrate surface, followed by subsequent hydration in the etchant solution and final product removal. The solubility of the products and the action of the polishing pad and abrasive are all critical to the passivation of the surface and the production of a polished substrate. The pH dependence of sodium hypochlorite is explained in terms of its composition. At low pH (<8) the main component of the etchant solution is dichlorine. At high pH (>8) the main component of the etchant solution is hypochlorite anion. Thus hypochlorite solution may be considered as a parallel to dibromine at low pH, but is more consistent with the behaviour of hydrogen peroxide at high pH. Thus, aqueous sodium hypochlorite solution may be formulated as part of the series O-O, O-X, X-X, where X represents a halogen. The General Model for Chemomechanical Polishing is formulated on the basis of the three stages of reaction observed for all the reagents examined: Oxidation of the substrate; solvation/hydration of the oxidation products; removal of the products from the substrate surface. Novel bromine-based organic reagents have been designed, synthesised and used to etch and polish gallium arsenide and cadmium telluride substrates. These compounds have shown that properties such as stock removal rate, pH dependence and selectivity may be predicted and even designed into etchants to produce the optimum conditions for polishing a given substrate.

Four sets of NIPAM and non-NIPAM based colloidal microgels have been synthesized by a surfactant-free emulsion polymerisation (SFEP) technique, which are: (i) poly (NIPAM) based homo-polymer, (ii) poly (NIPAM) based co-polymer, (iii) hydrophobically modified homo-polymer and (iv) hydrophobically modified co-polymer microgels. Poly (NIPAM) based homo-polymer microgels have been studied with respect to their heteroaggregation/heteroflocculation behaviour with oppositely charged polystyrene latex (PS) particles. It has been shown that the particle size, concentration and temperature play an important role in the ionic interaction between oppositely charged microgel and PS latex particles. Some particulate dispersions have shown temperature-dependent reversible flocculation behaviour, which could be applicable in the water industry for the removal of colloidal impurity from water. A strong irreversible aggregation was also observed for some microgel-latex mixtures, which may find useful application in the field of crude oil recovery. Hydrophobically modified homo-polymer and co-polymer microgels have been prepared from a range of novel monomers. The monomers have been chosen with varying hydrophobic chain length in order to manipulate the swelling properties of the resultant particles in different solvents. The dispersibility behaviour of the novel and NIPAM-based microgels has also been studied in different solvents to find their utility in removing water from oil. Colloidal microgel particles have shown successful application in reducing the water content of biodiesel to an acceptable level. Karl Fischer titration results have shown that water level in biodiesel can be reduced below 500 ppm from 1800 ppm by using microgel as water absorbent. According to the EN14214 specification by European Committee 500 ppm is the maximum water level allowed in biodiesel to be useful in combustion engine.

A combination of kinetic methods (primarily stopped-flow spectrometry) and computational modelling of the binding of hydroxamic acids to the active site of a model peroxidase (horseradish, LPO; myeloperoxidase, MPO) was used to provide insight into structure-function relationships of peroxidases. Hydroxamic acids acted as inhibitors of the native state (E), by formation of an E-hydroxamic acid complex that prevents H2O2 from binding. Hydroxamic acids donate one proton and one electron to peroxidase intermediates (CI and CII) and are oxidised to a radical themselves. It is likely that the proton of the hydroxamic acid group is transferred to the His residue via a H-bond network involving Pro139, His42, Arg38 in HRP and His109, Gln105, Asp108, Arg255 and Glu258 in LPO as the hydroxamic acid group of all substrates investigated was bound in the vicinity of these active site residues. However, ambiguity remains as to the precise mechanism of proton transfer. Two mechanisms were proposed for electron-transfer. Mechanism one involves the transfer of an electron to the solvent-exposed haem edge (i.e. δ-haem edge in HRP; D-haem edge in LPO). Mechanism two involves the transfer of an electron to an amino acid-residue situated at the opening of the substrate access-channel followed by long-range electron-transfer (LRET) to the active site (i.e. Phe68 in HRP; Pro115/Ala114→sheet A→helix 2 or Pro424→sheet E→helix 13 in LPO). Peroxidases are likely to be partially responsible for the inactivation of hydroxamic acid-based drugs in vivo. These data reported here may be considered in drug design.

Abstract In the UK, up to six million tonnes of potatoes are produced annually and more than half of this production is stored for the fresh market and food processing. To maintain potato quality from sprouting, chlorpropham (CIPC) is currently used as the main sprout suppressant in commercial potato stores. Questions have been raised about the safety of application of this compound in potato stores due to increasing concern about the toxicity of its residue and degradation products mainly 3-chloroaniline (3-CA) on the potato tubers. To date, there is no realistic replacement of CIPC for inhibiting sprouting of potatoes destined for processing. Searching for alternatives is crucial particularly as most supermarkets demand foods free of chemicals. The sprout inhibitor 1,4-dimethylnaphthalene (1,4-DMN) can be a suitable replacement for CIPC as it is naturally occurring in the potato and currently used in many countries in the world. To introduce this compound to the UK for commercial use, many investigations must be conducted to ensure its safety for human health and the environment. This study intended to focus on the determination of the residue level of 1,4-DMN, CIPC and its metabolite 3-CA in potato and water samples, hence developing analytical methods was required as a preliminary step. In this study, three HPLC systems were used for validating a separation method for the analysis of 1,4-dimethylnaphthalene and its internal standard 2-methylnaphthalene (2-MeN). Under the same chromatographic conditions, all these systems achieved excellent separation on a Jones-ODS column (Hypersil ODS 5 µm, 250 mm x 4.6 mm) at ambient temperature isocratically using 70% acetonitrile as mobile phase at a flow rate of 1.5 mL/min, 20 µL injection volume, a run time of 10 minutes and a detection wavelength of 228 nm. All three systems showed high precision (RSD% < 1%), good linearity of the calibration curves at two concentration ranges (0.02 – 0.1 and 0.2 – 1.0 µg/mL) of each 1,4-DMN and 2-MeN with coefficient of determination (R2) of the regression line of 0.990 or more. The best system SpectraSERIES UV100-autosampler system was selected for the remainder of this research as it offered lower values for both the limit of detection (LOD) (0.001 – 0.004 µg/mL) and the limit of quantification (LOQ) (0.002 – 0.013 µg/mL) for both compounds. A second isocratic reversed phase HPLC-UV method was developed and validated for analysis of 1,4-DMN and 2-MeN using methanol as a substitute solvent for standards and mobile phase preparations to overcome the problem of a global shortage of acetonitrile during 2008 – 2009. The best separation was achieved on the Phenomenex® (ODS-2 250 mm x 4.60 mm 5 µm Sphereclone) column using 90% methanol as mobile phase at a flow rate of 1.5 mL/min and a 6 minute run time. The method was validated producing good precision, linearity and low values of LOQ (~ 0.001 µg/mL). A straightforward and rapid isocratic HPLC-UV method was developed and validated for the simultaneous analysis of both CIPC and its degradation product 3-CA using methanol as a solvent and propham (IPC) as an internal standard. To achieve high resolution of the three compounds, the chromatographic conditions selected were: Phenomenex® column (ODS-2 250 mm x 4.60 mm 5 µm Sphereclone), 62% methanol at a flow rate of 1.5 mL/min, detection wavelength of 210 nm and a 15 minute run time. Method validation confirmed good precision, acceptable linearity and low values of LOD (~ 0.01 µg/mL) and LOQ (~ 0.04 µg/mL) for CIPC and 3-CA. These proposed HPLC methods are suitable to apply for the determination of the studied compounds in both potatoes and water samples. Quantitative laboratory analysis of 1,4-DMN, 2-MeN , CIPC and 3-CA in water solutions showed acceptable standard preparations in water with good precision and linearity and lower values of LOD and LOQ close to those obtained in organic solvent preparations. An adsorption study of 1,4-DMN and 2-MeN on laboratory ware showed that glass materials were acceptable to use whereas there was a considerable adsorption to plastic containers and filters. In contrast, 3-CA showed no adsorption onto any of the laboratory ware tested. CIPC also showed good recoveries with most of the materials tested. In reviewing the literature, no suitable published method for the simultaneous determination of CIPC and its metabolite 3-CA in potato peel was found. A simple analytical method was developed based on methanol-soaking overnight extraction coupled with HPLC-UV for analysis of CIPC and 3-CA in potato samples using IPC as internal standard. The method was validated and the calculated limit of quantification was 0.01, 0.05 and 0.02 µg/g in whole tuber for CIPC, IPC and 3-CA respectively. The efficiency of the method reported recovery values of up to 90% for both CIPC and IPC through spiking organic potato peel at three spiking levels of 0.8, 8.0 and 80 µg/g. By contrast, 3-CA recoveries offered very low values of 10 and 23% at concentration levels of 8.0 and 80 µg/g respectively and no peak was detected at the lower level of 0.8 µg/g. This method was compared with the routine Soxhlet-GC method used for the analysis of the residues of CIPC in potato samples at the University of Glasgow laboratory and gave results approximately 23% higher residues of CIPC. This new method at this stage was suitable to extract CIPC in 20 potato samples daily. Nevertheless, an interesting finding was that despite the low recovery of 3-CA it was identified in treated potato samples. This unanticipated low recovery is noteworthy and indicates that the actual residue may be much higher. A comprehensive study was made to improve the extractability of 3-CA from potato samples investigating parameters including potato variety, extracting solvent, extraction method, spiking procedure and different treatments for potato samples. All these experimental trials showed no recovery improvements, thus four possible mechanisms were suggested for poor recovery of 3-CA including volatilisation, reaction with potato components, enzymatic activity and ion exchange related to pH. Under the laboratory work experimental conditions, no measurable loss of 3-CA by volatilisation was found. No reaction of 3-CA was found to occur with other potato components under the experimental conditions used. However, the Schiff base reaction and/or hydrogen bonding may link the amino group of 3-CA and some functional groups abundant in potatoes (e.g. carbonyl, quinone). This study also showed a potential role for enzymatic activity in the poor recovery of 3-CA. Using antioxidants or acidity to inhibit this enzymatic activity was shown to enhance the extractability of 3-CA. Binding of 3-CA to potato peel substrates by ion exchange is unlikely as the pKa value of 3-CA is lower than the pH of the potato. However, using sulphuric acid combined with methanol as an extracting solution improved the recovery. Optimising the extraction process showed that using a mixture of 1 M H2SO4 in 50% methanol as an extracting solution for 24 hours at 50 ºC improved the extraction recovery of 3-CA up to 85%. This final extraction method was applied for the determination of the residues of both CIPC and 3-CA in commercial potato samples which had received many applications of CIPC, thus reporting high residue values. Additionally, potato samples were taken from different UK stores for the storage season 2010 – 2011 which had received CIPC application at high and low temperature (450 ºC and 270 ºC respectively) fogging. Analysis of these potato samples showed no significant difference between high and low temperature for the first application of CIPC for both residues of 3-CA and CIPC. A significant increase in both compounds was found between the first and second application at 270 ºC indicating a possible build up with time during storage.